Shaun,
You could always export your current system junction feature class to another new feature class, then delete your existing network dataset (which would delete the original system junction feature class as well), and rebuild it using your new point feature class as a custom junction feature class. This would allow you to keep the original point data as a single junction feature class, but would also allow you the flexibility to add new fields, etc. to your custom junction feature class (since the network dataset would not manage your new custom junction feature class as a "system junction" class; you would be allowed to edit it as you see fit). Does this make sense?